Mon 24 Dec 07:38:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl6-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:38:30 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-3.6-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1263 and 0 Target number of residues in the AU: 1263 Target solvent content: 0.6504 Checking the provided sequence file Detected sequence length: 388 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1552 Adjusted target solvent content: 0.57 Input MTZ file: 1vl6-3.6-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 12416 target number of atoms Had to go as low as 0.85 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 124.815 3.600 Wilson plot Bfac: 78.40 22267 reflections ( 99.87 % complete ) and 0 restraints for refining 13813 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3364 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3408 (Rfree = 0.000) for 13813 atoms. Found 88 (88 requested) and removed 287 (44 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.30 Search for helices and strands: 0 residues in 0 chains, 13891 seeds are put forward NCS extension: 0 residues added, 13891 seeds are put forward Round 1: 545 peptides, 102 chains. Longest chain 15 peptides. Score 0.308 Round 2: 724 peptides, 114 chains. Longest chain 18 peptides. Score 0.419 Round 3: 779 peptides, 111 chains. Longest chain 23 peptides. Score 0.473 Round 4: 786 peptides, 101 chains. Longest chain 25 peptides. Score 0.512 Round 5: 804 peptides, 108 chains. Longest chain 23 peptides. Score 0.502 Taking the results from Round 4 Chains 106, Residues 685, Estimated correctness of the model 0.0 % 13 chains (98 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25368 restraints for refining 11247 atoms. 22411 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2933 (Rfree = 0.000) for 11247 atoms. Found 72 (72 requested) and removed 150 (36 requested) atoms. Cycle 2: After refmac, R = 0.2856 (Rfree = 0.000) for 10916 atoms. Found 66 (71 requested) and removed 121 (35 requested) atoms. Cycle 3: After refmac, R = 0.2616 (Rfree = 0.000) for 10669 atoms. Found 69 (69 requested) and removed 90 (34 requested) atoms. Cycle 4: After refmac, R = 0.2535 (Rfree = 0.000) for 10548 atoms. Found 68 (68 requested) and removed 76 (34 requested) atoms. Cycle 5: After refmac, R = 0.2490 (Rfree = 0.000) for 10426 atoms. Found 67 (67 requested) and removed 67 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 10811 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 10824 seeds are put forward Round 1: 718 peptides, 119 chains. Longest chain 15 peptides. Score 0.396 Round 2: 829 peptides, 113 chains. Longest chain 28 peptides. Score 0.504 Round 3: 840 peptides, 117 chains. Longest chain 23 peptides. Score 0.499 Round 4: 864 peptides, 119 chains. Longest chain 29 peptides. Score 0.510 Round 5: 854 peptides, 113 chains. Longest chain 22 peptides. Score 0.522 Taking the results from Round 5 Chains 117, Residues 741, Estimated correctness of the model 0.0 % 11 chains (83 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 24013 restraints for refining 11004 atoms. 20905 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2757 (Rfree = 0.000) for 11004 atoms. Found 70 (70 requested) and removed 91 (35 requested) atoms. Cycle 7: After refmac, R = 0.2754 (Rfree = 0.000) for 10818 atoms. Found 70 (70 requested) and removed 97 (35 requested) atoms. Cycle 8: After refmac, R = 0.2511 (Rfree = 0.000) for 10674 atoms. Found 69 (69 requested) and removed 61 (34 requested) atoms. Cycle 9: After refmac, R = 0.2408 (Rfree = 0.000) for 10599 atoms. Found 68 (68 requested) and removed 57 (34 requested) atoms. Cycle 10: After refmac, R = 0.2568 (Rfree = 0.000) for 10529 atoms. Found 68 (68 requested) and removed 61 (34 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 10939 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 10961 seeds are put forward Round 1: 744 peptides, 117 chains. Longest chain 23 peptides. Score 0.425 Round 2: 804 peptides, 107 chains. Longest chain 41 peptides. Score 0.506 Round 3: 826 peptides, 109 chains. Longest chain 35 peptides. Score 0.515 Round 4: 810 peptides, 103 chains. Longest chain 31 peptides. Score 0.523 Round 5: 855 peptides, 100 chains. Longest chain 30 peptides. Score 0.564 Taking the results from Round 5 Chains 107, Residues 755, Estimated correctness of the model 0.1 % 10 chains (118 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 24133 restraints for refining 11251 atoms. 20823 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2638 (Rfree = 0.000) for 11251 atoms. Found 72 (72 requested) and removed 103 (36 requested) atoms. Cycle 12: After refmac, R = 0.2525 (Rfree = 0.000) for 11084 atoms. Found 71 (71 requested) and removed 80 (35 requested) atoms. Cycle 13: After refmac, R = 0.2521 (Rfree = 0.000) for 11018 atoms. Found 71 (71 requested) and removed 83 (35 requested) atoms. Cycle 14: After refmac, R = 0.2267 (Rfree = 0.000) for 10926 atoms. Found 70 (70 requested) and removed 58 (35 requested) atoms. Cycle 15: After refmac, R = 0.2188 (Rfree = 0.000) for 10890 atoms. Found 70 (70 requested) and removed 59 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 11272 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 11298 seeds are put forward Round 1: 740 peptides, 131 chains. Longest chain 13 peptides. Score 0.371 Round 2: 840 peptides, 120 chains. Longest chain 28 peptides. Score 0.489 Round 3: 841 peptides, 118 chains. Longest chain 20 peptides. Score 0.496 Round 4: 831 peptides, 113 chains. Longest chain 21 peptides. Score 0.506 Round 5: 810 peptides, 109 chains. Longest chain 22 peptides. Score 0.503 Taking the results from Round 4 Chains 115, Residues 718, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25212 restraints for refining 11251 atoms. 22332 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2436 (Rfree = 0.000) for 11251 atoms. Found 72 (72 requested) and removed 65 (36 requested) atoms. Cycle 17: After refmac, R = 0.2352 (Rfree = 0.000) for 11158 atoms. Found 66 (72 requested) and removed 69 (36 requested) atoms. Cycle 18: After refmac, R = 0.2217 (Rfree = 0.000) for 11081 atoms. Found 58 (71 requested) and removed 59 (35 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2307 (Rfree = 0.000) for 11039 atoms. Found 71 (71 requested) and removed 56 (35 requested) atoms. Cycle 20: After refmac, R = 0.1900 (Rfree = 0.000) for 11008 atoms. Found 19 (70 requested) and removed 42 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 11350 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 11376 seeds are put forward Round 1: 716 peptides, 129 chains. Longest chain 17 peptides. Score 0.358 Round 2: 767 peptides, 120 chains. Longest chain 19 peptides. Score 0.433 Round 3: 785 peptides, 114 chains. Longest chain 19 peptides. Score 0.468 Round 4: 781 peptides, 109 chains. Longest chain 18 peptides. Score 0.482 Round 5: 790 peptides, 113 chains. Longest chain 20 peptides. Score 0.475 Taking the results from Round 4 Chains 110, Residues 672, Estimated correctness of the model 0.0 % 7 chains (35 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25796 restraints for refining 11250 atoms. 23122 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2303 (Rfree = 0.000) for 11250 atoms. Found 72 (72 requested) and removed 66 (36 requested) atoms. Cycle 22: After refmac, R = 0.2251 (Rfree = 0.000) for 11180 atoms. Found 72 (72 requested) and removed 46 (36 requested) atoms. Cycle 23: After refmac, R = 0.2167 (Rfree = 0.000) for 11146 atoms. Found 61 (71 requested) and removed 43 (35 requested) atoms. Cycle 24: After refmac, R = 0.2091 (Rfree = 0.000) for 11115 atoms. Found 67 (71 requested) and removed 45 (35 requested) atoms. Cycle 25: After refmac, R = 0.2123 (Rfree = 0.000) for 11093 atoms. Found 66 (71 requested) and removed 53 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 11482 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 11503 seeds are put forward Round 1: 676 peptides, 123 chains. Longest chain 24 peptides. Score 0.345 Round 2: 792 peptides, 124 chains. Longest chain 23 peptides. Score 0.439 Round 3: 780 peptides, 117 chains. Longest chain 24 peptides. Score 0.454 Round 4: 786 peptides, 114 chains. Longest chain 22 peptides. Score 0.469 Round 5: 785 peptides, 119 chains. Longest chain 27 peptides. Score 0.451 Taking the results from Round 4 Chains 119, Residues 672, Estimated correctness of the model 0.0 % 6 chains (52 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25257 restraints for refining 11253 atoms. 22512 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2430 (Rfree = 0.000) for 11253 atoms. Found 72 (72 requested) and removed 66 (36 requested) atoms. Cycle 27: After refmac, R = 0.2272 (Rfree = 0.000) for 11155 atoms. Found 72 (72 requested) and removed 58 (36 requested) atoms. Cycle 28: After refmac, R = 0.2212 (Rfree = 0.000) for 11126 atoms. Found 71 (71 requested) and removed 49 (35 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2175 (Rfree = 0.000) for 11105 atoms. Found 71 (71 requested) and removed 48 (35 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1863 (Rfree = 0.000) for 11095 atoms. Found 20 (71 requested) and removed 42 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.23 Search for helices and strands: 0 residues in 0 chains, 11428 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11448 seeds are put forward Round 1: 664 peptides, 120 chains. Longest chain 18 peptides. Score 0.346 Round 2: 751 peptides, 118 chains. Longest chain 24 peptides. Score 0.427 Round 3: 731 peptides, 110 chains. Longest chain 24 peptides. Score 0.439 Round 4: 766 peptides, 122 chains. Longest chain 23 peptides. Score 0.425 Round 5: 738 peptides, 106 chains. Longest chain 19 peptides. Score 0.459 Taking the results from Round 5 Chains 108, Residues 632, Estimated correctness of the model 0.0 % 7 chains (49 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 26000 restraints for refining 11253 atoms. 23455 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2409 (Rfree = 0.000) for 11253 atoms. Found 72 (72 requested) and removed 53 (36 requested) atoms. Cycle 32: After refmac, R = 0.2412 (Rfree = 0.000) for 11202 atoms. Found 72 (72 requested) and removed 54 (36 requested) atoms. Cycle 33: After refmac, R = 0.2334 (Rfree = 0.000) for 11168 atoms. Found 71 (71 requested) and removed 46 (35 requested) atoms. Cycle 34: After refmac, R = 0.2278 (Rfree = 0.000) for 11124 atoms. Found 71 (71 requested) and removed 45 (35 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2238 (Rfree = 0.000) for 11115 atoms. Found 62 (71 requested) and removed 47 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.20 Search for helices and strands: 0 residues in 0 chains, 11509 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 11534 seeds are put forward Round 1: 605 peptides, 122 chains. Longest chain 12 peptides. Score 0.284 Round 2: 691 peptides, 122 chains. Longest chain 14 peptides. Score 0.362 Round 3: 707 peptides, 117 chains. Longest chain 15 peptides. Score 0.394 Round 4: 728 peptides, 115 chains. Longest chain 20 peptides. Score 0.419 Round 5: 710 peptides, 112 chains. Longest chain 19 peptides. Score 0.415 Taking the results from Round 4 Chains 115, Residues 613, Estimated correctness of the model 0.0 % 6 chains (27 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 25858 restraints for refining 11255 atoms. 23440 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2519 (Rfree = 0.000) for 11255 atoms. Found 72 (72 requested) and removed 75 (36 requested) atoms. Cycle 37: After refmac, R = 0.2407 (Rfree = 0.000) for 11180 atoms. Found 72 (72 requested) and removed 59 (36 requested) atoms. Cycle 38: After refmac, R = 0.2330 (Rfree = 0.000) for 11152 atoms. Found 71 (71 requested) and removed 47 (35 requested) atoms. Cycle 39: After refmac, R = 0.2269 (Rfree = 0.000) for 11140 atoms. Found 71 (71 requested) and removed 51 (35 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2315 (Rfree = 0.000) for 11122 atoms. Found 64 (71 requested) and removed 45 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.20 Search for helices and strands: 0 residues in 0 chains, 11508 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11525 seeds are put forward Round 1: 558 peptides, 117 chains. Longest chain 13 peptides. Score 0.259 Round 2: 665 peptides, 122 chains. Longest chain 16 peptides. Score 0.339 Round 3: 672 peptides, 118 chains. Longest chain 17 peptides. Score 0.361 Round 4: 699 peptides, 114 chains. Longest chain 16 peptides. Score 0.399 Round 5: 676 peptides, 110 chains. Longest chain 14 peptides. Score 0.394 Taking the results from Round 4 Chains 115, Residues 585, Estimated correctness of the model 0.0 % 7 chains (47 residues) have been docked in sequence ------------------------------------------------------ 22267 reflections ( 99.87 % complete ) and 26020 restraints for refining 11253 atoms. 23642 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2439 (Rfree = 0.000) for 11253 atoms. Found 72 (72 requested) and removed 59 (36 requested) atoms. Cycle 42: After refmac, R = 0.2407 (Rfree = 0.000) for 11189 atoms. Found 72 (72 requested) and removed 64 (36 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2393 (Rfree = 0.000) for 11151 atoms. Found 71 (71 requested) and removed 49 (35 requested) atoms. Cycle 44: After refmac, R = 0.2234 (Rfree = 0.000) for 11137 atoms. Found 71 (71 requested) and removed 45 (35 requested) atoms. Cycle 45: After refmac, R = 0.2276 (Rfree = 0.000) for 11135 atoms. Found 71 (71 requested) and removed 48 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.22 Search for helices and strands: 0 residues in 0 chains, 11491 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 11513 seeds are put forward Round 1: 535 peptides, 112 chains. Longest chain 14 peptides. Score 0.257 Round 2: 622 peptides, 116 chains. Longest chain 13 peptides. Score 0.324 Round 3: 625 peptides, 110 chains. Longest chain 14 peptides. Score 0.350 Round 4: 628 peptides, 106 chains. Longest chain 14 peptides. Score 0.368 Round 5: 613 peptides, 100 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 100, Residues 513, Estimated correctness of the model 0.0 % 6 chains (25 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vl6-3_warpNtrace.pdb as input Building loops using Loopy2018 100 chains (513 residues) following loop building 6 chains (25 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22267 reflections ( 99.87 % complete ) and 26455 restraints for refining 11255 atoms. 24446 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2420 (Rfree = 0.000) for 11255 atoms. Found 0 (72 requested) and removed 36 (36 requested) atoms. Cycle 47: After refmac, R = 0.2266 (Rfree = 0.000) for 11148 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 48: After refmac, R = 0.1964 (Rfree = 0.000) for 11077 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.1872 (Rfree = 0.000) for 11018 atoms. TimeTaking 127.17